Status of Coral Reefs of the World: 2025

1. Introduction

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2. Code

Cleaning and selection (`a_`)

a01_select_benthic-data.R Extract benthic cover data from gcrmndb_benthos.
a02_clean_intersect-reefs.R
a03_benthic-data_sources.R Extract lists of datasetID and contributors details.
a04_clean_buffer-reefs.js Create coral reef buffer polygons at 5, 20, 50, and 100 km using GEE.
a05_clean_cyclones.R Clean cyclones data.
a06_download_crw-year.R

Indicators’ extraction (`b_`)

b01_extract_population.js Extract population indicators using GEE.
b02_extract_crw.R Extract SST indicators.
b03_extract_cyclones.R Extract cyclones indicators.
b04_region-characteristics.R Extract region characteristics.

Models (benthic cover) (`c_`)

c01_explo_benthic-data.qmd Exploratory analyses of benthic cover data.
c02_select_pred-sites.R
c03_extract_predictor_gee.js
c04_extract_predictor_gravity.R
c05_extract_predictor_enso.R
c06_extract_predictor_cyclones.R
c07_extract_predictor_crw.R
c08_model_data-preparation.R
c09_xgboost-model.R
c11_format-results.R

Figures and tables (`d_`)

d01_geography-maps.R
d02_spatio-temporal.R
d03_cyclones.R
d04_crw.R
d05_population.R
d06_reef-extent.R
d07_benthic-cover_trends.R
d08_case-studies.R

Writing and sharing (`e_`)

e01_generate_docx.R
e02_authors-contribution.R

Functions

data_descriptors.R Get number of sites, surveys, datasets, first and last year of monitoring.
docx_chapter.Rmd Template to generate the .docx regional chapters.
docx_supp-mat.Rmd Template to generate the .docx Supplementary Materials.
extract_coeff.R Extract slope from linear regression.
graphical_par.R Graphical parameters, including colors and fonts.
map_region_geography.R Map of region (geography).
map_region_monitoring.R Map of region (monotoring).
map_sphere.R Map of region (sphere).
plot_trends_model.R Plot temporal trends from models.
plot_trends_raw.R Plot temporal trends from raw data.
prepare_benthic_data.R Prepare benthic cover data for models.
styles.docx Word documents styles
theme_graph.R Main ggplot theme for the plots of the reports.
theme_map.R Main ggplot theme for the maps of the reports.

3. Reproducibility parameters

Warning in system2("quarto", "-V", stdout = TRUE, env = paste0("TMPDIR=", :
l'exécution de la commande '"quarto"
TMPDIR=C:/Users/jerem/AppData/Local/Temp/Rtmp0ks32V/fileaf0db8509b -V' renvoie
un statut 1
─ Session info ───────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.5.2 (2025-10-31 ucrt)
 os       Windows 11 x64 (build 26200)
 system   x86_64, mingw32
 ui       RTerm
 language (EN)
 collate  French_France.utf8
 ctype    French_France.utf8
 tz       Europe/Paris
 date     2025-12-23
 pandoc   3.6.3 @ C:/Program Files/RStudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown)
 quarto   NA @ C:\\PROGRA~1\\RStudio\\RESOUR~1\\app\\bin\\quarto\\bin\\quarto.exe

─ Packages ───────────────────────────────────────────────────────────────────
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 [1] C:/Users/jerem/AppData/Local/R/win-library/4.5
 [2] C:/Program Files/R/R-4.5.2/library

──────────────────────────────────────────────────────────────────────────────

Name		Name	Last commit message	Last commit date
Latest commit History 102 Commits
code		code
misc		misc
.gitignore		.gitignore
README.Rmd		README.Rmd
README.md		README.md
global_2024.Rproj		global_2024.Rproj

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Status of Coral Reefs of the World: 2025

1. Introduction

2. Code

Cleaning and selection (`a_`)

Indicators’ extraction (`b_`)

Models (benthic cover) (`c_`)

Figures and tables (`d_`)

Writing and sharing (`e_`)

Functions

3. Reproducibility parameters

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Status of Coral Reefs of the World: 2025

1. Introduction

2. Code

Cleaning and selection (a_)

Indicators’ extraction (b_)

Models (benthic cover) (c_)

Figures and tables (d_)

Writing and sharing (e_)

Functions

3. Reproducibility parameters

About

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Cleaning and selection (`a_`)

Indicators’ extraction (`b_`)

Models (benthic cover) (`c_`)

Figures and tables (`d_`)

Writing and sharing (`e_`)

Packages